Far in the future earth is dependent on silicon for it's technology. Unfortunately the silicon reserves are running out. A new source of silicon has been located in a faraway part of the galaxy. Problem is that it's very dangerous to gather since it has a tendency to explode. Therefore a mercenary going by the name of Sillo is sent to the location with a vehicle known as the silicon fisher to gather this necessary yet dangerous material.

3D Silicon Fish consists of a maze that is located above a river that floats from the top to the bottom of the screen. The player navigates through the maze with his vehicle while looking for silicon that floats with the stream. Collecting the silicon is done by positioning the vehicle towards the part where the silicon will pass and throwing out a net to catch it. The player is however not alone in the maze. Around him something called kryllon forms out of thin air and explodes after a short while. If the player then is within range of the explosion he will be killed.